Maze Runner 3 - Nobody Get's Left Behind
by Ninjaboy13779546
Summary: The Gladers, Brenda, and Jorge make it to The Last City but come across two surprises on their trek to stop WCKD and save Minho. Will they make it back with everyone, or will they lose some? Alternate Version of Maze Runner 3.
1. Hey Greenie, Hey Thomas

**Hey guys, I literally just saw The Death Cure and I gotta say... WOW! Just wow. It was great, super emotional but I wasn't impressed with all the main character deaths. So thanks to the power of imagination and fanfiction, I've found a way to save them. And I'm bringing back another original character. So here we go!**

* * *

 *****Last City, Secret Base*****

Brenda had just calmed Jorge down. But he had good reason to be riled up. Him, The Gladers, and Brenda had just been thrown into trucks and taken to someplace they didn't know.

"Everybody relax, we're all on the same side here," The leader said.

"What do you mean 'same side'? Who the hell are you?" Thomas asked defiantly.

The leader stopped and slowly turned towards Thomas. After hesitating slightly, he pulled off his mask to reveal that it was Gally.

"Hey Greenie," He said before dropping his mask to the floor.

Everyone's eyes widened. How was this possible? "Gally?" Thomas said unbelievingly.

"No way," Frypan said shaking his head.

The last time they saw Gally, he had them at gunpoint but was killed when Minho threw a spear at him. He died right in front of them, so how was he here, standing right in front of them, very much alive?

Remembering their last encounter, Thomas stormed towards Gally and landed a punch on the right side of his face, make Gally fall to the ground. Thomas jumped on top of him and continued to try and hit him. Seeing this, the other Gladers, Brenda, and Jorge tried to tell Thomas to stop, but he didn't listen. The soldiers readied their gun but another one ran towards the two to try and pull them apart, as did Newt.

"Thomas, stop! Stop!" He said pulling his friend back. But Thomas didn't budge.

"He killed Chuck," Thomas said, reminding Newt of what happened when they left the Glade. In the mix, Gally had accidentally shot Chuck. When Thomas said this, the soldier that was holding him back, stood up and backed away.

"Yeah, I know. I remember I was there." Newt replied, "But I also remember, that he was stung and half out of his mind. Just calm down."

After Newt said that, Thomas jumped back but kept his fists clenched. Gally slowly got up and felt his jaw to make sure that it wasn't broken and was still in place.

"Kinda had that comin'," He said as he took a breath, "Anybody else? Fry? Newt?"

"You know this guy?" Jorge asked.

"He was an old friend," Frypan replied emphasizing the 'was'.

"How? How is this possible?" Newt asked, "We watched you die."

"No, you left me to die. And if we hadn't found you when we did, you'd be dead right now. What the hell are you doin' here?"

"Minho, WCKD has him here. We're looking for a way in."

After thinking for a second, Gally looked at them and said, "I can help with that. Follow me."

"I'm not going anywhere with you," Thomas interjected.

"Look, Thomas, I know it may be hard for you. But you need to trust us." A muffled voice said.

Everyone looked to see where the voice came from. It came from the soldier who had held Thomas back when he had Gally pinned to the ground. They didn't get a good look at him before, but looking at him now, they noticed that he was hefty looking with a full head of curly hair.

"Who the hell are you?" Thomas asked, "And how do you know my name?"

The soldier let out a muffled sigh and hung his head down. He lifted his head and looked towards Gally.

"Should I?" He asked

Gally shrugged his shoulders. "Might as well, I showed my face."

Nodding, the soldier lifted his hands to his mask, took it off, and dropped it on the ground. He ruffled up his hair a bit before lifting his head and showing face to the Gladers, Brenda, and Jorge. Once again, their eyes widened as they saw that the mysterious soldier was none other than the youngest Glader from the Maze, Chuck.

"Chuck?" Thomas whispered unbelievingly.

"Hey Thomas," He said showing a little smile.

When he spoke to him, Thomas' breath got stuck in his throat. He couldn't believe this, his best friend from the Maze was alive along with Gally. Wait, Gally? Thomas looked at Gally again with a look that could kill.

"Chuck, get away from him," He said motioning for him to come over, "He's the one who shot you back at the Maze."

"I know," Chuck replied as he walked over to Gally and put a hand on his shoulder, "I also know that WCKD was controlling Gally when he was trying to shoot you and they were controlling me to jump in front of you."

Thomas shook his in disbelief. This couldn't be real this had to be a joke. That's what kept telling himself until he saw Chuck starting to walk towards him.

"I know it's a lot to take in. With everything that's going on, I understand," He said as he got close enough to hug his old friend, "But right now, you need to listen to Gally and trust us. We can help you, and he won't do anything to hurt you. I've been working with him all this time and we're still good. So, what do ya say?"

Thomas had to think long and hard about this. He didn't really want to Gally, but at this point, they didn't have that many options. This was their only chance... unfortunately.

"Ok," He said, reluctantly nodding his head.

"Alright, good," Gally said, "Now if you guys wanna stay here and get killed, then suit yourself. But if you come with me and Chuck, we can get you through those walls."

All eyes went to Thomas. Sure he'd said yes to Chuck, but Gally outranked him, so he had more sayso. After mulling it over in his head, Thomas let out a sigh and looked at Gally with a look that said 'Fine'.

* * *

 **BOOM! How was that for the beginning of a story or the middle of a movie? I wanted to write this on account of them bringing Gally back. I figured, if they could bring Gally back, why not bring Chuck back too? But since they didn't, I'm gonna do it. Also, this is gonna be a bit different from the movie. I'm gonna find a way for everyone to live, and still have an emotional ending. And I might do a sequel if I can think of a good plot. So hope this will hold you over** till **the next chapter. Later, Gladers!**


	2. A Way In

**Ok, one chapter in and I got a pretty good response to it and I wanna thank you guys for that. For all you fellow Thomesa fans out there, I have an idea for four more Maze Runner/Thomesa stories. The first three are prequels beginning with a small oneshot before the first two movies, the next two would follow Movie 1 & 2, and the last one would be a sequel to The Death Cure. I'd start the first one right when Thomas wakes up after from stinging himself in the first Maze Runner. He'd remember who he was and tell Teresa and she'd kiss him because she felt something between them too, and then I'd work it up from there. Let me know what you guys think in the comments. And now, the next chapter!**

* * *

 *****Last City, Secret Base*****

"After the Maze, we got picked up by a group that was headed to the city," Gally started as he and Chuck guided the Gladers, Branda, and Jorge through the base, "They realized we were immune, patched us up, and then brought us here. To Lawrence."

"Who's Lawrence?" Thomas asked.

"He's our leader, he's the one who helped save us after you guys left the Maze," Chuck explained, "He's also kinda creepy, so don't stare directly at him."

He whispered the last part before Gally continued his story.

"This group's been at war with WCKD ever since they took over the city. But WCKD can't hide behind those walls forever. Day's gonna come when they're gonna pay for what they've done."

They kept walking until they came to a dark section of the base and Gally stopped them.

"Listen uh, he doesn't get a lot of visitors," He explained, "So let me and Chuck do the talking. And try not to stare."

When Gally walked away, their eyes went to Chuck because he'd said the same thing earlier. But in secret. When he saw them staring at him, he shrugged his shoulders and said, "Told ya," before he walked ahead to follow Gally with a small chuckle. They looked at each other before reluctantly following the two.

They all walked in to see a guy standing next to another man in a cloak who was talking to some flowers and trimming them. He was connected to an IV bag that was hanging on a stand. When he saw them come in, he stood up fully and greeted them.

"Gally, Chuck, glad to see you two made it back," He said, "Jasper here told me what happened."

"It was a slaughter," Gally explained, "There's nothin' we can do against those guns."

"Yeah, when they opened fire, the best we could do was try to get as many civilians away as possible. We saved but... Not everybody made it. "Chuck added.

"It's alright, you guys did the best you could. As for WCKD well, they can only poke the hornet's nest for so long, before they get stung." Lawrence said as he sniffed one of the flowers, "Who are these people, and why are they here?"

"They're some old friends of me and Gally's when we were trapped in the Maze," Chuck explained, "They got out just before you guys found us, I guess."

Lawrence listened and nodded his head as he messed with the flower in his hand some more. "Ok, so why are they here?"

"We need to get into WCKD," Thomas stated, "Gally says that you can get us through those walls."

When he heard this, Lawrence put the flower down and slowly turned his head to look at them. "Well Gally should know better than to make promises he can't keep." He said, "'Sides, that wall is only half your problem. Getting inside WCKD is impossible."

"There might be a way now," Gally reasoned, "But it doesn't work without Thomas."

Thomas turned his head toward Gally in both shock and surprise. The only time he ever heard Gally say his real name was in anger. But things were different now, maybe this would work. Maybe.

"Is that so?" Lawrence replied as he stepped forward. When he came into the light, they saw that the right half of his face was loaded with bulging veins and soars. And his nose seemed to be gone all the way down to the skeleton. Now they knew what Gally and Chuck meant when they said 'Don't stare'.

"Do you know what I am, Thomas? I am a businessman, which means that I don't take unnecessary risks. So why should I trust you?"

"Because I can help you," Thomas replied, "You see, if you can get me and my friends through those walls, I can get you what you need."

"And what is it, that you think I need?"

"Time, every last drop of it."

Thomas motioned at Lawrence's IV bag to further his point. Lawrence took a step back and looked at it, then to Gally. Deep down, he knew this kid was right. He didn't know how much time he had left, this may be his last and only chance.

"Is that what I need?" It was more of a sarcastic statement that a question, but the others understood perfectly.

"WCKD has something that we both want, and we're gonna do whatever it takes to get it back."

"I tell ya what, two can go now, the rest stay here." Lawrence offered, "There's still no assurance you'll make it back. We have a deal?"

He extended his hand that wasn't as bruised as his face, but it still looked bad. But that didn't stop Thomas from taking and shaking it.

"Gally, Chuck, show them the way."

Gally pulled back a metal lid which covered a big hole in the ground. Chuck came over with a ladder and gave it to Gally who slowly lowered it down the hole until it reached the bottom. Once it was situated, Chuck went down first, then Gally.

Just before he got all the way down, Frypan called him. "Take care of these two."

Gally nodded before he continued his descent. A couple of feet away, Newt was straightening his shoes when he looked at his hands and saw what he was afraid of. But he ignored it and followed the others down the hole.

* * *

Well **there's the second chapter. I wanted to put Gally's story in there because it seemed a good way for Chuck to still be alive too. Don't worry, Thomesa drama is coming soon! Also, I'm still wondering if I should bring Brinho into this story or not. Let me know because I'm also thinking about putting in some Aris & Sonya and Gally & Harriet in there. My mind is just going right now. So let me know what you think and I'll see you guys in the next chapter.**


	3. Feelings

**Ok, Chapter 3 is here. Gonna have some hard decisions, drama, and more Chuck. I had to think hard to find parts where he could fit in and I almost didn't make it. But fortunately, I was able to work it out just enough. So, hope you guys enjoy this.**

* * *

 *****Secret Tunnel*****

"Ok so let me get this straight," Chuck started, "After you guys escaped WCKD, ran halfway around the world trying to hide from them, Teresa just up and betrayed you guys?"

"Yeah, that's about the size of it," Newt replied.

"Well, I hate to say 'I told you so', well, actually no I don't," Gally added, "I knew that girl was trouble from the moment she woke up."

"Gally, come on. It wasn't until WCKD got a hold of her and messed with her mind that she betrayed them."

"Yeah but she still betrayed 'em, Chuck. So really it doesn't make much of a difference."

"Ok can we just focus here, please?" Thomas asked, "Where are you taking us, Gally?"

"It's right through here."

Gally ran up to a door and opened it slowly to make sure there was no security on the other side. Seeing that there was opened the door and they all walked right into a sea of people walking in the city. Some had masks on, hoping that it would help them not catch the virus, but some didn't.

Gally and Chuck led Thomas and Newt up a set of stairs where they got a clear view of the city. It was beautiful, so many buildings, so many lights.

"Well, this is a long way from the Glade," Newt stated.

"Yeah, look we gotta get off these streets," Gally said, "I know it's hard but, it ain't like you never seen it before."

Chuck let out a chuckle as he followed his friend. The two Gladers look at each other before following the other two.

* * *

 *****Streets*****

The four ran across a street and lean against a glass wall to hide fro a security van that passed by.

"They definitely upped security," Gally whispered, "I'm guessin' you shanks have something to do with that."

"Oh really, what gave it away?" Chuck asked with a laugh, "The fact that they started shooting at the gates, or that there are more guards and vans?"

"Keep it down, Chuck. Come on let's get outta here."

They started running again and headed towards the outskirts of the city. When they stopped, Thomas and Newt realized that they had made it to the walls. Gally got down and put his hands together to help them up. First Newt, then Chuck(Which was much harder to do, but still doable), then he got back down for Thomas.

But Thomas, still not fully trusting Gally just said, "I got it," and grabbed onto the ledge and pulled himself up. Then Gally did the same.

***The City Wall***

The four ran down a path along the walls until they came to a doorway within the wall and went through it. As they did, it led to a set of stairs that went up to the top. When they came up, they were at the top of the wall and could almost see everything.

"There it is," Gally said as he pointed to a building in the center of the city that lit up brighter than any building in the city, WCKD headquarters. "If WCKD's got Minho, that's where he is."

Chuck walked over to a mat and pulled out a kaleidoscope and handed it to Gally. Gally took it and set it on a stand they had set on the railing and looked through it.

"Lawrence has been trying to find a way in for years," He said, "But the place is crawling with soldiers. They got surveillance everywhere. Scanners on every floor."

"Sounds like a bloody fortress," Newt added.

"Damn right," Chuck said.

"And you've got a way in?" Thomas asked Gally unbelievingly.

"I might."

"You might? What the hell do you mean 'might'?"

Gally looked at Thomas and sighed before he backed up and gestured to the scope. "Take a look," He said.

Thomas walked over and looked through it, but what he found on the other side shocked him. He saw Teresa, working in a lab. Still beautiful as the day when he first saw her in the Glade. Backing away from the scope, Thomas understood now. Gally wanted to use Teresa to get the into WCKD.

"I said I had a way in, but I didn't say you were gonna like it," Gally said when Thomas looked back at him.

Thomas looked back out onto the city and let out a long sigh.

* * *

 *****Secret Base*****

The group had been contemplating using Teresa as a way in, and everybody agreed to it. Everybody except for Thomas of course. He tried his best to think of another way, but he couldn't. Everything he thought of came back to Teresa and her being used.

"No, there's gotta be another way," He said.

"Like what, man?" Gally scoffed, "You've seen the building, she's our only way in."

"You really think she's gonna help us?"

"Well I don't plan on asking her for permission."

"Am I missing something here?" Brenda cut in, "This is the same girl who betrayed, correct? Same d*ck?"

"Oh I like her," Gally said pointing at Brenda, "Why couldn't we have had her back in the Glade?"

"Cause you two probably would have killed with your craziness," Chuck replied with a laugh.

Brenda just shook her head to ignore the two and focus on the mater at hand. "Seriously Thomas, what's going on?"

Thomas was silent because he knew the answer to her question, but was to scared to admit it.

"What? Are you afraid your little girlfriend's gonna get hurt?" Newt interjected in a tone that was foreign to him. It was kinda angry/cranky. "Hmm? This has obviously never been just about rescuing Minho. Right?"

"Wh-What're you talking about?" Thomas asked.

"Teresa! She's the reason Minho's even missing in the first place, now we have to get him back and you back. And, what you don't because of her?! Because deep down you still care about her don't ya? Just admit it."

"Newt, I don-"

But Thomas was cut off when Newt grabbed him and shoved him against the wall. "DON'T LIE TO ME! DON'T, LIE, TO ME!"

The sudden outburst shocked everybody. Newt had never done this before, yelled at anyone. He was always gentle and kind and occasionally sarcastic. But this wasn't like him.

He kept starring at Thomas until he blinked and started panting like he'd been running. He let go of Thomas and backed away with a look of horror at what he'd done to his friend.

"Sorry...Sorry," he said as he walked out of the room and headed outside.

* * *

 **Well that's it for this chapter. Sorry for taking so long, but I've been busy with my job and work on Fast 9 and also another story that I'm producing at this point called JL -DC(Daycare). It's gonna be based on the Justice League movie but with a younger daycare AU twist. So you'll find out about it soon. But for now, until next chapter, this is Ninja-Boy, signing off.**


	4. All Good

Thomas walked out to see Newt sitting on the edge of the roof. Slowly, he walked up to him so as not to alarm him in case he might have another outburst. Sensing someone behind him, Newt turned his head to see Thomas standing there.

"Sorry about that in there," He said as he went back to twiddling his thumbs. After letting out a sigh, he pulled back his left sleeve to reveal his arm which had bulging black veins. Signifying that he had the Flare virus. "I guess I can't hide this anymore."

Thomas knelt down and nodded, understanding what was now. This is why Newt was having mood swings of aggression, and why he let one out in the meeting that they and the others just had.

"Why didn't you tell me?" Thomas asked in a more caring and understanding tone.

"Didn't think it would make any difference if I did," Newt stated, "God knows WCKD must've put me in that Maze for a reason. Maybe it was literally just so they could know the difference between immunes like you and people like me."

The way Newt said that tore Thomas apart. What did Newt mean people like him? They were the same. It'd been almost a year since they left the Glade, and Newt was just starting to get the Flare, so why hadn't the others?

Maybe it was that Crank that jumped on him in that abandoned mall that triggered it... Maybe. Regardless of how Newt got the Flare, Thomas knew he had to do something.

"We can fix this, Newt," He said with a new sound of hope in his voice, "Ok? We can."

"Don't worry about me," Newt replied also with hope in his voice, "This is about Minho, and now he needs us. So if there's even the slightest chance that we can save him, to get him out, then we have to take that. No matter what the cost."

Thomas knew that he was right, and even though he still wasn't up to doing it, he was gonna do it. "Ok, I hear ya."

The two then sat in silence and looked at the walls the contained the city. Hoping that this plan would work.

"Hey," a voice called out behind them.

The two turned around to see Chuck walking towards them.

"Everything ok out here?" He asked, "You guys hash out everything?"

Thomas looked at Newt and then smiled at his friend. "Yeah, we're all good." He said.

"Ok, good to hear," Chuck replied as he headed back in.

"Hey Chuck!" Thomas called out, "Come're, buddy.

The plumpy teen walked back to his friends. When he did, Thomas handed him something. When he looked at it, he froze. It was the wood carving that he gave Thomas just before he... Just before he died.

"Wow, I'm surprised you still have this," Chuck said.

"What do ya mean?"

"Well I figured being the shank that you are, you'd have lost it by now."

That made all three of them laugh, they missed this. The last time they had a moment like this was back in the Glade. Maybe when all this was over, they'd be able to have more moments like this.

"Here Thomas, I gave it to you for keeps, I want you to have it," Chuck said handing it back to Thomas.

"You sure?" Thomas asked.

"Yeah. Chances are my parents aren't alive anymore. So, keep as like, something to remember me by."

Thomas then took it out of Chuck's hands then hugged him. "Thanks, Chuck. I promise you that we're all gonna make it out of this alive."

"I know," Chuck replied. He knew Thomas always kept his promises, so he hoped that this time wouldn't be any different. Hopefully.

* * *

 **TOO MUCH EMOTION! This is what I love about writing, you can express yourself in any way. And I expressed myself through making a scene that could fit Chuck. So I'm gonna keep doing this til the end of this story, making funny yet emotional scenes for Chuck like the ones he did in the first movie. Also, I need to know, Should I make a Maze Runner 4 story? I kinda have an idea of what it could be, but I want you guys to let me know if I should. So, til next chapter, Ninja-Boy out!**


	5. Regret

**Ok this is where the rubber meets the road, where Thomas and Teresa meet finally reunite in the city, and the others interrogate her. This is the part I wanted to do for a long time, cause it's so emotional and really brings out a lot of Thomesa drama. Sooooooooooooooo, here we go.**

* * *

Teresa stood at the edge of the crosswalk, still traumatized by the events that happened earlier. Another failed attempt, another loss. The little girl was so innocent, so full of life and desire to live. But now she was gone, and Teresa couldn't do anything about it. Now all she could do was go home and try to sleep this off.

A bus passed by in front of here and when it did, she saw a face she never expected to see again... Thomas. Her eyes widened when she saw him standing across the street. He was wearing a backpack and a hoodie, undoubtedly trying to keep a low profile. But still, why would he come here of all places? Alone?

Another bus passed by. She was afraid when it did, Thomas would be gone. Just a figment of her imagination. Perhaps her guilt playing with her mind. But when the bus did pass, she still saw Thomas. Only he was walking away.

Teresa immediately followed him, hoping to catch up with him. She followed him into a crowd of people and into a subway station. Soon she was within a sea of people and had lost sight of Thomas. It wasn't until the crowd cleared up a bit that she saw the hooded boy walking away again and she started to follow him.

"Thomas?!" She called out, hoping he would answer. But all he did was look back at her before disappearing into a back hallway. She followed him in there, but only to find the hallway empty.

But she really saw him come in here, or maybe her guilt HAD been playing with her mind. But it seemed so real. She kept looking around until she felt the presence of someone behind her. She slowly turned around and was face to face with her boyfriend. Or ex-boyfriend? She didn't even know, neither did he. But it didn't matter now. He was here, right in front of her.

"Thomas," she said again, but this time with more sadness and regret in her voice.

"Hi, Teresa," He replied. It'd been so long since she heard his voice. She missed it. That same voice that used to say 'I love you' or 'Everything's gonna be ok'. That same voice that didn't sound so happy right now.

"You shouldn't be here." She shook her head with fear of what would happen. Despite that she was happy to see him, she didn't want any harm to come to him. "If Janson finds out he'll-"

"I'm not staying. It's just umm...I had to see you."

He needed to see her? Did he really just say that? Maybe he missed her too and wanted to work things out, or maybe he was here to end things. But why bother, they're as good as done. So why would he risk his life to come here?

"I had to ask you somethin'." Thomas continued,"...Do you regret it, what you did to us?"

'It'? She knew exactly what he meant by 'It'. And boy, did that stir up some emotions up in her. It wasn't even a question of if. Of course she regretted it. She lost everything in one fell swoop. Her friends, her family, her best friend...Her boyfriend, and his trust.

"Sometimes," She admitted, "...But I did what I thought was right, and I'd do it again."

Surprised to her, Thomas didn't seem phased by her answer at all. In fact, he just nodded and said, "Good."

He shifted his eyes behind her and before she knew it, a bag was over her head, put there by Gally who secured it.

* * *

 *****Secret Base*****

The bag was pulled off her head and Teresa looked around until she saw the person who pulled it off, but when she saw him, she felt a cold chill go down her spine. It was someone she hadn't seen since they left the Maze, someone she thought was dead. She saw him walk over to a round table where the rest of the group was sitting.

"Gally?" She said, finally finding her voice which was mixed with both confusion and shock.

"Oh wow, she remembered," Chuck said with a bit of sarcasm, "I thought she might've forgotten us."

"Chuck?" More shock and confusion could be heard.

"Yup, it's me. Been a long time, Teresa." Even though he still considered Teresa a friend, Chuck was also pissed at her for what she did to his friends.

"H-H-How're you...BOTH, still alive? You shot him and you got impaled."

Before Chuck could explain, Gally interjected.

"Look we can settle the meet and greet later. We've got more important matters to talk about."

Chuck knew Gally was right, looks like he was gonna have to wait another time to tell the story.

"Ok, here's how this is gonna go," Gally said throwing down some papers onto the table, "We're gonna ask you some questions, and you're gonna tell us exactly what we need to know."

Teresa looked around to try and get a good look at the place, but her vision came upon Thomas who was still sitting at the table. She kept her gaze on him as she heard Gally continue.

"We'll start off simple," He said picking up a chair, "Where's Minho?"

"You guy's don't seriously think that-"

(SLAM) She stopped and changed her gaze to Gally when he slammed a chair in front of her and sat in it, blocking her view of Thomas.

"Don't look at him. Why're you lookin' at him? Look at me! He's not gonna help you."

And he was right, Thomas didn't even flinch when Gally said those words. He just sat and watched the events play out. Hoping that Gally wouldn't get too out of hand, 'cause he was just starting to trust the shank again.

"Now we know you have Minho in the building, where?"

She thought for a moment. She was in a tight spot right now. She was risking a lot. But something inside her felt like telling was the right thing to do."He's with the others in holding, Sublevel 3."

"How many others?' Newt asked, jumping in.

"...28."

The group looked over to Brenda who was playing cards with herself. "I can make that work," She said placing another card down.

"No, no you guys don't understand, the whole level is restricted," Teresa stated, "You can't get in without a thumbprint ID."

"That's why you're gonna help us," Thomas said, finally speaking up, "You're gonna come with us."

"Well I don't know," Gally said, sardonically shrugging his shoulders, "We don't necessarily need her, right?"

Gally stood up and moved his chair before grabbing a scalpel from the table, instantly making Chuck jump up. "Remember our talk, Gally," He said trying to calm his tall friend down.

"What? We really don't need her. Not all of her, we just need her finger."

"Gally back off," Thomas said.

"What's wrong, you squeamish? I guarantee you, she's done a lot worse to Minho."

Thomas shook his head as he stood up and took the scalpel out of Gally's hand.

"It's not the plan, back off."

"It won't make a difference," Teresa said, redirecting their attention to her, "You still won't get through the front door. The sensors'll pick you up from the sec-"

"We know, we're tagged. 'Property of WCKD.'" He knelt down in front of her and held the scalpel up, "You can help us with that too."

* * *

***1 Hour Later***

Teresa picks up the scalpel again and positions it at the back of Thomas' neck.

"Just try to relax, this is gonna sting," She said.

"Let's just get it over with," Thomas replied.

After he said that, he felt a slight itchy feeling in the back of his neck before the sting that Teresa mentioned came and he winced in pain. Having punctured the skin, she grabbed a cloth and applied it to the cut.

A couple feet away, Gally kept an eye on them as he held a cloth to the back of his neck. "She enjoyed that," He stated, throwing his cloth onto the table.

"You prolly right," Frypan said in agreement.

Newt walked by with a couple of coats and gave one to both of them. "Here, see if these fit."

"Thanks."

"Thanks, Newt."

* * *

"She's looking good, healthy," Teresa said looking at Brenda who was watching Jorge walk out, "How've you been getting a serum?"

"What're you talkin' about?" Thomas asked.

"Brenda, I didn't think she'd still be alive. When was her last treatment?" She asked as she started to pull out the WCKD Tracking clip with a pair of tweezers.

"Right Arm, last time we saw you."

That made Teresa freeze. The last time she saw them? How could that be possible? "But that was months ago."

As she was in her daze, she didn't realize that she pulled the whole tracking slip out quickly, making Thomas jolt forward. He looked back at her with a look of somewhat annoyance.

"Thomas, that's not possible, she should've turned by now. There's no way she could possibly be-"

"That's enough," Thomas said getting up and walking away, but Teresa, still curious, put the surgical tools down and followed suit.

"You don't believe me?" It was more of a statement than a question, but she sure got one helluva answer when Thomas turned around and looked her right in the face.

"You really expect me to?" He said with a tone that made her heart crack, "You made your choice."

She should've expected that reaction. He was still mad because of what she did. Just like Newt said, he still cared about her, but that doesn't justify what she did. And she knew that, but still wanted to help him, but she also wanted to help save the world. maybe in this, she could do both. Finish her mission, AND redeem herself. But most importantly, get her man back. They held their gazes at each other until Gally came over.

"Everything OK over here?" He asked.

Thomas and Teresa held their gazes for just a bit longer before Thomas let out a sigh.

"Yeah, yeah we're done," He said walking away.

As he did, Teresa had an idea. Looking over her shoulder, she saw reached over the surgical tools, but her hand was stopped by none other than Gally.

"Nice try," he said as he guided her out.

As they walked, Teresa looked down at her hands to see the blood-stained cloth that Thomas used and stuffed it in her pocket.

* * *

Thomas walked over to Brenda who was cleaning and preparing guns for the mission.

"You're in love with her, right?" She asked Thomas.

Thomas, already knowing the answer, was still somewhat confused. With what Teresa had done to them, and how he felt, he was a constant conflict with himself. So he just replied with a simple, "I don't know."

"Just be careful," Brenda continued as she handed him his gun," You have this problem where you can't walk away from people, even when you should. You can't save everyone, Thomas."

Thomas nodded. She was right, he knew he couldn't save everyone. Even though he wanted to. "But I can try," He replied.

Having said her piece, she walked off to finish prepping herself. Thomas mulled over what she said. It was something that he was afraid of. But he had hope, and for now, that would have to do. Shaking off his bad thought, he cocked his gun and holstered it, ready for action.

* * *

 **MY FINGERS HURT! This was a long chapter, but it was worth it. Loaded with Thomesa drama and more Gally and Chuck. I'm really having a lot of fun doing this story and I can't wait until I'm done so that I start on Maze Runner 4 and more Thomesa. And then maybe Fast & Furious 10, still need to think of what I'm gonna name it. But for now, I think this is good. So until next chapter, this is your friendly neighborhood Ninja-Boy saying, Adios!**


	6. Inside The Heart Of The Monster

**Ok, sorry for taking so long to update, but the infiltration of WCKD and more Thomesa drama is here. Also, not sure if you noticed, but I made a new cover poster for the story with the main cast. Thomas, Teresa, Newt, Minho, Chuck, Gally, and Frypan. So let's get right into it!**

* * *

 *****WCKD Tower*****

Teresa walked towards the entrance of WCKD Tower with a masked guard alongside her. She looked at him with a nervous look, like this wasn't going to work. But then again, she always looked a Thomas that way. Even now, when the stakes were much higher than they've ever been, he still had hope that this would end well.

They both entered into the lobby which had quite a few guards in it.

"Go slow," Thomas said as they passed the guards.

And as they walked through security scanners, the light on it blinked green. That took a load off their shoulders, mainly Thomas'. As they walked further down the hallway, another masked guard walked up to them. His uniform was slightly different from the one Thomas was wearing. His was a dark navy blue with black pretty much everywhere. However, this guard had a bit more red on his uniform. It was mainly on the arms and legs, but it still looked cool.

The guard stared at both of them for a while. An uneasy feeling stirred up inside of them. Had they been found out? Was this the end? Their worried minds were calmed when they saw the guard motion for them to follow him. It was Newt! He'd gotten in an hour earlier than them so that he could meet them without it seeming so obvious.

As they walked down a staircase and into a glass hallway, another guard joined them from the other side of the glass wall that opened into a parking garage. They kept walking until they came to a heavy-duty security door. Knowing that this was her cue, Teresa stepped forward and unlocked the door with her security pass. On the other side of the door was a stairwell and they headed down.

"Hold on, hold on. I can get in here." They heard the other guard say. It was Gally, and he was looking at a series of electrical boxes. Pulling off his mask, he went to work on getting it open.

"Here, throw me the walkie," Thomas said, to which Gally tossed a walkie to him and he walked down the stairwell to scope out where they were going. Newt and Teresa stayed behind with Gally. As they waited, Newt began to cough. He felt lightheaded like he was gonna pass out. Teresa noticed this and stared at him in realization. She understood why they also wanted the serum, to help save Newt. He was infected, it all made sense now.

Hearing a power saw-like noise, she looked to her left and saw Gally drilling into the electrical boxes. Thomas came walking back up the stairs towards them with his walkie up. "Frypan, we're in. How you doin'?"

* * *

 *****Construction Crane Latter*****

Frypan climbed up another step before stopping.

"Yeah. Yeah, I'm gettin' there," He nervously replied into the walkie as he looked up to see that he had a lot more climbing to do. "Tell Minho 'hi' for me."

 _"Hang in there, bud,"_ Thomas said on the other end.

Taking a deep breath, Frypan resumed climbing.

* * *

After drilling for a few more seconds, Gally opened the box to find a bunch of wires, conduits, and smaller boxes. All were labeled, so Gally searched them until he found the one he was looking for.

"This one," He said looking at Thomas.

Thomas nodded back before talking into the walkie again, "Brenda, Chuck, what's your status?"

* * *

 *****Garage*****

Brenda and Chuck knelt down in front of a bus to keep out of sight of a nearby group of guards.

"Status is, we're workin' on it," the tanned girl replied into her walkie.

"And I may have also klunked my pants," Chuck chuckled, "But other than that, status is good."

 _"Copy, just make sure you guys are ready on your end,"_ Thomas said back.

Seeing that the coast was clear, the two started walking towards a row of idle buses.

"Oh don't worry, you know I'm gonna be there," Brenda said reassuring her brunette friend.

"Be careful up there, Thomas," Chuck added.

 _"Thanks, Chuck. You too."_

As that was said, the two ran through a maze of busses to get to their destination.

* * *

Gally connected a device to the wires, placed it the door of the electrical box, and closed it.

"Alright, let's go!" He said.

The group headed down the stairs, onto another floor and headed down another hallway until Teresa showed them the one that held the immune kids. Before Teresa could use her keycard, the door opened, revealing a guard on the other side.

Swiftly, the fired their weapons, to which the other guards fired their guns. With the bullets nearly missing them, the group was able to disable the guards. Having done so, Newt walked over to one of the cells, looked in and saw a few kids. As he opened it, the kids backed away out of fear. They didn't know he was good 'til he pulled off his mask and smiled.

"Come on, let's go," he said motioning for them to follow, "Come on."

"It's OK, you guys 're OK," Thomas said opening the next cell. The kids slowly walked out, hoping that they wouldn't hurt them. While they walked out of the cell, Thomas and Newt checked to make sure they were all OK.

As they checked them, Gally picked up a half-conscious guard off the ground and shook him. "The vault, how do I get in?" He asked.

"You can't," the guard hoarsely replied before Gally let him drop back onto the floor.

Walking over to the vault, Gally inspected it to try and find a way in. It was thick, obviously. But more than that, the density of it was amazing. Not in a good way, more like in a 'OH COME ON!' type of way.

"Guys, this is might take some time." He said as he prepared to cut his way in.

Meanwhile, Thomas was going through the cells looking for Minho, but he couldn't find him. "Sh*t, he's not here." He said walking over to Teresa, grabbing her by the shoulders, "Where is he?"

Teresa thought hard to remember. Minho was WCKD's prize right now, and they were injecting and extracting blood and fluids from him nonstop. So where would he be? Thinking quickly, she ran to the computer, typed in Minho's identity, and hit ENTER. A few seconds later, the screen brought up a map of the building to show them where Minho was.

"Somebody's moved him up to the medical wing," She said in a surprised tone, "Thomas, that's on the other side of the building."

Thomas nodded in understanding grabbing his helmet and gun. "Alright, take me to him, right now. Come on."

"Alright, I'm comin' with you," Newt said walking with them.

"Newt, no you're not. You have to stay here with Gally and wait for the serum."

Newt looked at Thomas dumbfounded and with determination. "You can't do this on your own. Minho comes first, remember?"

"Just go, we're wasting time!" Gally said, pausing his drilling, "I'll get the serum and we'll meet you out back."

Reluctantly, Thomas agreed. "Alright, let's go."

Pulling Teresa along with them, they started walking when Gally called out to Thomas. "Hey Greenie! Good luck."

Thomas nodded before catching up with Teresa and Newt as they headed back up to the main floor.

* * *

 *****Main Floor*****

"Keep moving," Thomas said as they neared an elevator.

As they waited, Thomas inconspicuously looked behind him to see a guard slowly walking towards them. Feeling a little more nervous, Thomas pushed the button again rapidly. As if that was gonna make the elevator come any faster. Finally, it arrived and the doors opened and they all filed in.

Pressing the floor number they wanted, the doors started to close. But just before they were fully closed, a hand poked through and pushed open. It was Janson! Teresa didn't let it show but she felt her heart skip a beat as he stepped in, as did Thomas and Newt's Thomas, feeling the rage flow through him, tightened his grip on his weapon. Just in case.

"You're working late," Janson said to Teresa.

Teresa replied with a smile and a nod. She was worried that if she spoke, she might give herself away.

"That's what I like about you, Teresa. No matter how bleak things get, you...Well...You never give up. Times like this, you need a friend that you can count on."

"I'll bear that in mind," Teresa replied, still trying to keep her cool.

It was silent for a few seconds. But within those few seconds, fear, anger, and determination were in the air. And it was strong. After those seconds were gone, Janson spoke again. " There is one thing you should know. One friend to another. Thomas is here."

This sent a chill go down both Thomas and Newt's spine as they looked at each other through their helmets. Regardless of how much they wanted to blurt something out, the two stayed silent and listened to the people in front of them.

"A surveillance picked him up outside the walls. " Janson continued, " Ava didn't want you to know, but there is a chance that he may try to contact you, and if he does, I'd like to think that I'd be your first call."Are you gonna kill him?" Teresa asked defiantly.

"Will that be a problem?"

Before she could answer, the elevator stopped on their floor. "This is me," She said stepping out. Thomas and Newt followed her with Thomas purposely bumping his shoulder against Janson's. As the doors closed, Teresa spoke freely. "Thomas, you have to listen to me. Getting that serum won't save Newt. It might buy him some time, but..."

"Just ignore her. She's trying to get inside your head." Newt said.

"Thomas, listen. You know what's going on out there. People are dying. The world is dying. There's something about your blood I don't understand."

"Open it," Thomas said, ignoring her words.

"If you let me run some tests...I promise I can protect you." Teresa pleaded through a tearful voice.

"Yeah? Like you protected Minho?" Her ex-lover retorted, flinging off his helmet, revealing a mad face.

"What are you doing?" Newt grabbed Thomas' shoulder, but he just shrugged his hand off and turned back to Teresa.

"How many people is it gonna take? How many more people do they have to round up, torture, kill? Huh? When the hell does it stop?"

"It stops when we find a cure."

"There is no goddamn cure!"

The two stared into each other's eyes, looking for some bit of remorse, a chance, maybe even love. But the moment was cut short when they hear a familiar voice shout out, "Don't waste your breath, Teresa. He made his choice long ago."

Teresa turned around to see Janson walking towards them with a gun in his hands. Thomas and Newt swiftly pulled up their guns and pointed it at Janson and was ready to fire when they heard more voices. Looking around, they saw guards coming at them from both sides and some more from behind Janson.

Thinking quickly, Thomas grabbed Teresa and held the gun to her head. "Back up. Tell them to back off. Tell them to back off!"

"Hey, Thomas, come on. It's me. I've known you longer than you can remember. You're not gonna shoot her."

"You don't think so?"

"Okay. Go on then. Shoot her. Prove me wrong."

Part of Thomas wanted to, but deep down, he knew he couldn't do it. He could never hurt Teresa. Newt was right, he still cared about her...He still loved her.

"Shoot her," Janson repeated.

Before Thomas could do anything, Teresa broke free and pushed Thomas and Newt back before closing the door that connected them. Seeing this, the guards opened fire until they realized the glass was bulletproof. Janson ran up to it and banged against it in anger.

But Thomas looked toward Teresa, who looked back at him with a small smile as if to say, 'Go get'em, love'. After sharing their stare for a while longer, Thomas and Newt ran off to find Minho. As they did, Janson looked at Teresa with a look that made mad look like an understatement.

"Your story better be good." He said between his teeth.

"I just did you a favor," Teresa said, motioning to the door, "Doors are sealed. They can't get out." She walked off with a determined look in her eyes. Before she got any further, she called out, "Janson, I need them alive."

After she said that, Janson stormed off to find the kid who annoyed him SO much. Teresa resumed walking, heading toward her lab. Pulling out the cloth that she used to clean Thomas' blood when she extracted his WCKD tag, hoping that her theory was right.

And as she walked, she felt as though she had gained a bit more love from Thomas. Maybe, just maybe, he felt the same. Litlle did she know, that as Thomas was running to find Minho, the thought had crossed his mind too.

* * *

 **Thomesa is rising again! My fingers are killing me from typing this whole chapter and I'm sorry it took SOOO LONG, but hey, I'M BAAAAACK! I'll upload on this again soon, but the next story I'll update is my Fast 9 story. Also, I'm producing a few new stories right now. One of them being a Maze Runner 4, although I need to think of a good title for it. Give me some ideas guys. So that's it for now, I also have a MASSIVE Romanogers oneshot coming soon. So for now, this is your friendly neighborhood Ninja saying, "I'M OUT!"**


	7. WCKD Crazy

**I'm back again, shanks! I'm so happy to be back in this fandom, AND with the Thomesa ship. So let's get into this!**

* * *

 *****WCKD Tower*****

Thomas and Newt were walking down a hallway full of doctors, trying not to be conspicuous.

And they were doing fine until they came across an intersection when Thomas saw Ava Paige standing down the hallway to his left. Immediately, rage began to build up in him as the two stared at each other.

Newt looked back just in time to see Thomas pull out his gun and aimed it for Ava. He wasn't sure what to do. Stop Thomas or let him pull the trigger. But his decision was made for him when he saw Janson pass down the hallway, but he stopped and pulled out HIS gun.

"Thomas!" He yelled as grabbed his friend and pulled him away just before Janson and the guards with him started firing.

They ran down the opposite direction, passing screaming doctors who were trying to take cover and kept an eye out for any guards.

"Minho!" Thomas called out.

Right after he did, some guards ran around a corner towards them. Thomas shot one of them just as he stepped forward. Newt covered him as he ran the other way before his friend joined him.

"Minho!"

They kept on running and dodging guards before Thomas' rifle ran out and he pulled out his gun and fired.

A guard came from behind them, but Newt saw him and shot him. They kept firing before they took cover around a corner.

Thomas checked his clip and was pissed with what he saw. "Sh**, I'm almost out."

Thomas shoved the clip back in the gun before he looked down the other hall and fired back, trying to buy them some more time.

As he did, Newt looked down at the guard he shot and started looking for something to help them. When he looked in the guard's bag, he saw what looked like a grenade. He activated it and yelled, "Get back!" before throwing it down the hall right in the middle of all the guards.

It went off, sending electric shocks everywhere. Including the guards.

"Nice." Thomas said as they resumed trying to find Minho.

"Alright, lets go!" Newt added.

But they were stopped by a guard in a hallway connection.

"You two, FREEZE!" He commanded. "Get down on the ground now!"

Thomas and Newt had nowhere else to go. This was it.

"I said get you a-!" Was all the guard got out before he was bumped aside by an angry Minho.

The two other Gladers were shocked as they watched their friend pin the guard against the wall and let out what seemed like screamed with rage before picking him and throwing him through a glass window into a lab. That guard was out for the count.

Minho took deep breaths before looking up to what looked like his friends. They ran up to him and embraced him with hugs and smiles.

"Is this real?" He asked, thinking WCKD could still be messing with his mind.

But he was reassured when they nodded. The reunion was cut short when they saw guards coming up behind them quick.

"RUN!" Thomas yelled.

They ran down another hallway until some guards came around that bend. Looking around, he saw a room.

"In here!" He said as they ran inside and locked the door.

They heard banging on the other side.

"Newt, come on!" Minho said as he walked over to a metal shelf.

Together, they moved it and flipped it over in front of the door. Backing up, they stood by Thomas. Trapped in a room with one way in and one way out. No! They needed to find another way out.

As they searched, they heard a loud grinding sound. Looking towards the door, they realized it was a saw. Janson and the guards were almost in.

Thomas began thinking again and looked around. His eyes fell upon the big glass window that led to the outside of the building.

"Any ideas?!" Minho asked behind him.

Thomas looked back to them with an unsure face. "Yeah...maybe."

He saw a large tank on the side and motioned for Minho to help him. Once in hand and over their shoulders, the two ran towards the window, bashed the tank through it and watched as it and the rest of the window fell to into a fountain below.

The three Gladers looked down. Nervous, skeptical and tired.

"Ok, it's doable." Thomas said, trying to keep their spirits up. "Just needs uh...a running start."

Newt and Minho watched as he walked over to the door to get a good distance. With no other choice, they followed.

"You sure about this?" Minho asked.

"Eh, not really."

A 'seriously?' look came onto Minho's face. "Nice pep talk."

"Yeah, we're all bloody inspired." Newt added sarcastically."

The door banged open with Janson right there. With no time left to think, the Gladers ran and jumped out the window.

"THOMAS!" Minho yelled as they fell.

"OOOH SHIIII-!" They splashes I to the fountain.

Back in he building, Janson looked out the broken window and saw the three come up. They all looked up and Thomas triumphantly flipped Janson off again.

They swam to the edge and helped each other out. But before they could run, the sound of guns cocking stopped them as they turned to see four guards.

"You three, don't move!" One of them ordered.

"Oh you gotta be kidding me." Thomas said. He knew this was gonna be a suicide mission, but COME ON!

He tried to reach for his gun, but they saw and told him to freeze.

But before any of them could fire, the guard on the far left turned and shot the others. The three were shocked at this and all eyes were on him. When the guard looked back to them, he walked up to them and took off his mask to reveal it was Gally.

"Gally?" Minho said, shocked and confused as heck.

The former Glader nodded to his former friend. "Minho." Looking up, he saw the window that they jumped from, which was extremely high. "You guys are nuts."

And with that, he walked off.

The Asian Glader stood there, still confused as ever. But Thomas just patted his shoulder and said, "I'll explain later," before he and Minho followed Gally.

But Minho was still frozen from confusion. He let out a sigh as he decided to let it go. For now.

* * *

 **Yeah, I know it's been like what...half a year since I updated this story. But I've had new stories come to my mind and I just wanted to go for them. But I never meant to leave this one behind. Especially because it holds one of my favorite ships, Thomesa.**

 **And believe it or not, I'm still working on Maze Runner 4. So please bare with me and I'll do my best to keep uploading as much as I can on these. The next chapter of Fast 9 will be up soon. Idk how soon, but it's like halfway done. So just keep your fingers crossed and it'll be here soon. I hope y'all enjoyed this, it was a long time coming. And more is coming. So until next chapter, NINJABOY OUT!**


End file.
